Here's how I do mine:
[1] Charge full, till green lights are lit
[2] Swap batts from one side/charger to the next - this will almost always result in red lights for the batts, even if previously charged to green (can't switch to discharge mode when fully charged / green light lit, for some reason).
[3] After you swamp them out, hit the discharge/charge buttons to discharge them. As Mike says, they'll flash yellow while discharging, then go to red while charging, then green when fully charged.
[4] Repeat [1]-[3] a couple/few times upon purchase, or every couple months.
[5] Off you go!